Receptor
PDB id Resolution Class Description Source Keywords
5X1V 2.1 Å EC: 2.7.1.40 PKM2 IN COMPLEX WITH COMPOUND 2 HOMO SAPIENS ACTIVATOR COMPLEX TRANSFERASE
Ref.: DISCOVERY AND STRUCTURE-GUIDED FRAGMENT-LINKING OF 4-(2,3-DICHLOROBENZOYL)-1-METHYL-PYRROLE-2-CARBOXAM PYRUVATE KINASE M2 ACTIVATOR BIOORG. MED. CHEM. V. 25 3540 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
7XX D:602;
C:602;
B:602;
A:602;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
297.137 C13 H10 Cl2 N2 O2 Cn1cc...
FBP A:601;
D:601;
C:601;
B:601;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
340.116 C6 H14 O12 P2 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2G50 1.65 Å EC: 2.7.1.40 THE LOCATION OF THE ALLOSTERIC AMINO ACID BINDING SITE OF MU PYRUVATE KINASE. ORYCTOLAGUS CUNICULUS ALLOSTERY PYRUVATE KINASE GLYCOLYSIS KINASE PHOSPHORYL TTRANSFERASE
Ref.: DIFFERENTIATING A LIGAND'S CHEMICAL REQUIREMENTS FO ALLOSTERIC INTERACTIONS FROM THOSE FOR PROTEIN BIND PHENYLALANINE INHIBITION OF PYRUVATE KINASE. BIOCHEMISTRY V. 45 5421 2006
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3BJF - FBP C6 H14 O12 P2 C([C@@H]1[....
2 4QG8 - MLI C3 H2 O4 C(C(=O)[O-....
3 4JPG - 1OX C16 H12 N4 O c1ccc2c(c1....
4 4G1N - NZT C24 H22 N6 O3 S c1cc2cccnc....
5 1A49 - OXL C2 O4 C(=O)(C(=O....
6 2G50 - PYR C3 H4 O3 CC(=O)C(=O....
7 5X1V - FBP C6 H14 O12 P2 C([C@@H]1[....
8 3N25 - PRO C5 H9 N O2 C1C[C@H](N....
9 1A5U - OXL C2 O4 C(=O)(C(=O....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3BJF - FBP C6 H14 O12 P2 C([C@@H]1[....
2 4QG8 - MLI C3 H2 O4 C(C(=O)[O-....
3 4JPG - 1OX C16 H12 N4 O c1ccc2c(c1....
4 4G1N - NZT C24 H22 N6 O3 S c1cc2cccnc....
5 1A49 - OXL C2 O4 C(=O)(C(=O....
6 2G50 - PYR C3 H4 O3 CC(=O)C(=O....
7 5X1V - FBP C6 H14 O12 P2 C([C@@H]1[....
8 3N25 - PRO C5 H9 N O2 C1C[C@H](N....
9 1A5U - OXL C2 O4 C(=O)(C(=O....
10 4IP7 - FBP C6 H14 O12 P2 C([C@@H]1[....
11 4IMA - FLC C6 H5 O7 C(C(=O)[O-....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3BJF - FBP C6 H14 O12 P2 C([C@@H]1[....
2 4QG8 - MLI C3 H2 O4 C(C(=O)[O-....
3 4JPG - 1OX C16 H12 N4 O c1ccc2c(c1....
4 4G1N - NZT C24 H22 N6 O3 S c1cc2cccnc....
5 1A49 - OXL C2 O4 C(=O)(C(=O....
6 2G50 - PYR C3 H4 O3 CC(=O)C(=O....
7 5X1V - FBP C6 H14 O12 P2 C([C@@H]1[....
8 3N25 - PRO C5 H9 N O2 C1C[C@H](N....
9 1A5U - OXL C2 O4 C(=O)(C(=O....
10 3QV9 - QV7 C22 H16 N4 O13 S4 c1cc(ccc1/....
11 3HQP - FDP C6 H14 O12 P2 C([C@@H]1[....
12 3QV8 - S62 C7 H5 N O6 S3 c1cc2c(cc1....
13 3PP7 - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
14 4IP7 - FBP C6 H14 O12 P2 C([C@@H]1[....
15 4IMA - FLC C6 H5 O7 C(C(=O)[O-....
16 4KCV - FDP C6 H14 O12 P2 C([C@@H]1[....
17 4KCT - PYR C3 H4 O3 CC(=O)C(=O....
18 4HYW - FDP C6 H14 O12 P2 C([C@@H]1[....
19 4KCU - MLT C4 H6 O5 C([C@H](C(....
20 4HYV - PEP C3 H5 O6 P C=C(C(=O)O....
21 4KCW - OXL C2 O4 C(=O)(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 7XX; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 7XX 1 1
Ligand no: 2; Ligand: FBP; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 FBP 1 1
2 AFP 1 1
3 F1X 0.744186 0.954545
4 TA6 0.666667 0.954545
5 F6P 0.666667 0.954545
6 FDP 0.462963 0.954545
7 OI7 0.448276 0.976744
8 F1P 0.418182 0.847826
9 AHG 0.404255 0.930233
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2G50; Ligand: ALA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2g50.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2G50; Ligand: ALA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2g50.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2G50; Ligand: ALA; Similar sites found: 13
This union binding pocket(no: 3) in the query (biounit: 2g50.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BSA NAP 0.04876 0.40953 2.31023
2 2BSA FAD 0.04735 0.40953 2.31023
3 1HV9 COA 0.02133 0.41043 2.85088
4 4ORM 2V6 0.04434 0.41813 2.99252
5 4ORM ORO 0.04434 0.41813 2.99252
6 4ORM FMN 0.04434 0.41813 2.99252
7 5BVE 4VG 0.02732 0.42727 3.04709
8 2CWH PYC 0.03648 0.40182 3.79009
9 2CWH NDP 0.03177 0.40039 3.79009
10 2BEK ATP 0.03172 0.40804 4.66926
11 4RSL FAD 0.0248 0.41362 5.61798
12 3O9L LPN 0.04548 0.40259 6.62651
13 1CLU DBG 0.04992 0.40131 31.9277
Pocket No.: 4; Query (leader) PDB : 2G50; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2g50.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2G50; Ligand: PYR; Similar sites found: 10
This union binding pocket(no: 5) in the query (biounit: 2g50.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JQN DCO 0.00742 0.43072 2.45283
2 4NAE 1GP 0.0236 0.41547 3.11111
3 4TX6 38B 0.01911 0.40673 3.87097
4 3DGB MUC 0.02069 0.40855 4.97382
5 1VDN ACE ALA ALA PRO ALA MCM 0.03164 0.41152 5.55556
6 2WSI FAD 0.01141 0.40132 5.55556
7 1O68 KIV 0.005028 0.45335 5.81818
8 5NBW 8SK 0.007874 0.42944 6.07477
9 1UJP CIT 0.009041 0.41532 6.27306
10 5M0T AKG 0.012 0.435 13.6054
Pocket No.: 6; Query (leader) PDB : 2G50; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2g50.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2G50; Ligand: ALA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2g50.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2G50; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2g50.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 2G50; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 2g50.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 2G50; Ligand: PYR; Similar sites found: 145
This union binding pocket(no: 10) in the query (biounit: 2g50.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3EWC MCF 0.0143 0.40542 1.34771
2 4JNA FAD 0.04378 0.40379 1.47059
3 3H22 B53 0.004195 0.43159 1.6835
4 3CV2 OXL 0.00009253 0.4808 1.69811
5 3MF2 AMP 0.01775 0.40636 1.7341
6 1AD4 HH2 0.009305 0.41378 1.8797
7 1P7T PYR 0.0005157 0.4262 1.88679
8 3W7T BMA 0.02221 0.41124 1.88679
9 3CQD ATP 0.01729 0.4258 1.94175
10 4JD3 PLM 0.02229 0.42363 1.983
11 4JD3 COA 0.02086 0.42363 1.983
12 4RW3 IPD 0.0111 0.40059 1.98676
13 1EE0 CAA 0.001808 0.47398 1.99005
14 1PIG AGL GLC HMC AGL GLC BGC 0.01876 0.42583 2.01613
15 4RFM 3P6 0.0166 0.43586 2.25564
16 2Y7G AAE 0.005934 0.43342 2.26415
17 3OIX FMN 0.01302 0.42123 2.31884
18 1D6H COA 0.01401 0.43595 2.32558
19 4OTH DRN 0.006996 0.43231 2.34604
20 2WU6 DKI 0.01468 0.41783 2.3622
21 1V0O INR 0.01095 0.4214 2.43056
22 4NMC 2OP 0.004193 0.46142 2.45283
23 4NMC FAD 0.004378 0.46142 2.45283
24 5X30 4LM 0.02201 0.40167 2.51256
25 5X30 7XF 0.0237 0.40011 2.51256
26 2B4G FMN 0.03132 0.40271 2.52366
27 4QIJ 1HA 0.03502 0.4276 2.69461
28 2X34 UQ8 0.04557 0.41153 2.76243
29 4YZN 4K5 0.006722 0.43965 2.78746
30 4I42 1HA 0.02128 0.40863 2.80702
31 3LL5 ADP 0.04656 0.40053 2.81124
32 3LL5 IPE 0.04656 0.40053 2.81124
33 1U08 PLP 0.002582 0.44264 2.84974
34 2WME NAP 0.01413 0.41843 2.85714
35 5U3F 7TS 0.02811 0.40392 2.98913
36 3S5Y DGJ 0.01743 0.40351 3.01508
37 3HAZ FAD 0.004833 0.45074 3.01887
38 1XRO LEU 0.03846 0.40035 3.07167
39 1LUA NAP 0.02823 0.40051 3.13589
40 1OVD FMN 0.03081 0.41232 3.21543
41 1OVD ORO 0.03081 0.41232 3.21543
42 5ULJ 0WD 0.008596 0.42985 3.2419
43 4K38 SAM 0.01546 0.40991 3.24324
44 4BHN BH9 0.01491 0.41557 3.29341
45 3QFU ADP 0.01811 0.40313 3.29949
46 1DBT U5P 0.01967 0.40044 3.34728
47 3SUD SUE 0.02182 0.40388 3.44828
48 1XKD NAP 0.03612 0.40264 3.44828
49 3DLS ADP 0.01611 0.40517 3.58209
50 2G37 FAD 0.004923 0.43235 3.58491
51 3TXO 07U 0.008526 0.42255 3.68272
52 2XZ9 PYR 0.0002439 0.4936 3.7037
53 4GA6 AMP 0.007937 0.41882 3.7037
54 1R6W 164 0.02433 0.40124 3.72671
55 5WX3 COA 0.008657 0.42996 3.77358
56 3HBN UDP 0.005206 0.43311 3.90071
57 2BUP ADP 0.02312 0.40847 3.93701
58 2BUP ATP 0.02312 0.40847 3.93701
59 4WB7 ATP 0.0338 0.41059 3.95062
60 1KC7 PPR 0.0001152 0.49487 3.96226
61 4DQ2 BTX 0.01373 0.43341 3.96341
62 1LBF 137 0.006488 0.44172 4.04858
63 1XJD STU 0.006021 0.43542 4.05797
64 5UOX 8GY 0.01524 0.41881 4.05904
65 2J9D ADP 0.01136 0.42433 4.20168
66 1C9K 5GP 0.00334 0.42998 4.44444
67 5DRB 5FJ 0.04555 0.41096 4.46735
68 5LI1 ANP 0.01135 0.42492 4.51977
69 4C2V YJA 0.02101 0.40814 4.5614
70 4WB6 ATP 0.02343 0.41012 4.57143
71 4L80 OXL 0.0001682 0.4725 4.5977
72 4JLS 3ZE 0.02679 0.40177 4.60526
73 2PI8 NAG NAG NAG NAG NAG NAG 0.04348 0.40148 4.63768
74 3O0Q TTP 0.02892 0.42293 4.71698
75 3O0Q ADN 0.02957 0.42293 4.71698
76 3O0Q GDP 0.02957 0.42293 4.71698
77 3EFS BTN 0.00572 0.44228 4.72103
78 3RJ5 NAD 0.04263 0.40391 4.72441
79 3HF3 FMN 0.03275 0.42484 4.87106
80 5KF6 TFB 0.006048 0.44871 4.90566
81 5KF6 FAD 0.006048 0.44871 4.90566
82 1N07 ADP 0.02353 0.41064 4.90798
83 1ERB ETR 0.02017 0.41006 4.91803
84 1FDJ 2FP 0.008889 0.4168 4.95868
85 1QS0 TDP 0.019 0.41339 5.02959
86 4B2Z P5S 0.007059 0.45545 5.13393
87 3LF0 ATP 0.003122 0.44916 5.26316
88 2IV3 UDP 0.03123 0.40209 5.26316
89 2AK3 AMP 0.01271 0.40062 5.30973
90 4RL0 3S0 0.0226 0.40369 5.3719
91 4X7Q 3YR 0.01353 0.41048 5.44872
92 1VJY 460 0.02436 0.41479 5.61056
93 4I9A NCN 0.01945 0.4049 5.90278
94 4TUO SIA GAL SIA GLC NGA 0.0225 0.40532 5.90909
95 4GID 0GH 0.01859 0.41909 5.92783
96 3E2M E2M 0.01607 0.40719 5.94595
97 2J3M ATP 0.01391 0.41448 6.03774
98 4QMN DB8 0.02534 0.41984 6.12903
99 1XAJ NAD 0.04207 0.40669 6.21469
100 1XAJ CRB 0.04207 0.40669 6.21469
101 2VWT PYR 0.0005482 0.45621 6.36704
102 4O8A FAD 0.006229 0.44572 6.41509
103 1TIW FAD 0.01046 0.43994 6.41509
104 1TIW TFB 0.01046 0.43994 6.41509
105 3AWJ COA 0.003657 0.44059 6.46766
106 3UXL CFI 0.03955 0.40912 6.52742
107 3MVH WFE 0.03004 0.40813 6.72515
108 1X1Z BMP 0.03214 0.41538 6.74603
109 1VBH PEP 0.000668 0.46599 6.79245
110 5A3T MMK 0.022 0.41858 7.06861
111 5M42 FMN 0.002199 0.44697 7.16846
112 3FMI KAP 0.03331 0.40212 7.17131
113 3MJY FMN 0.01661 0.4237 7.22543
114 3MJY IJZ 0.01661 0.4237 7.22543
115 5A5W GUO 0.03926 0.40848 7.50988
116 1MZV AMP 0.009197 0.41782 7.65957
117 4H6Q TFB 0.006796 0.43505 7.69231
118 4H6Q FAD 0.005729 0.43505 7.69231
119 3C3N FMN 0.02134 0.41987 8.33333
120 2WQP WQP 0.03905 0.40239 8.59599
121 3G6K FAD 0.007168 0.43882 8.76623
122 3G6K POP 0.006815 0.43882 8.76623
123 1U7Z PMT 0.01926 0.42963 8.84956
124 3UWV 2PG 0.01643 0.41811 9.1954
125 3O0G 3O0 0.0137 0.41123 9.39597
126 4L9Z COA 0.0008867 0.50019 9.43953
127 4L9Z OXL 0.0008372 0.50019 9.43953
128 4JEJ 1GP 0.01619 0.40196 9.83607
129 4WNP 3RJ 0.004546 0.44025 10.1045
130 3CY2 MB9 0.01167 0.42464 10.1911
131 1HYE NAP 0.009854 0.42578 10.5431
132 1IZC PYR 0.0001114 0.44259 10.6195
133 4MNS 2AX 0.04972 0.40754 10.6918
134 1FFU CDP 0.005799 0.45896 11.0429
135 2V5K OXM 0.000104 0.49599 11.4983
136 4H2W AMP 0.01491 0.40042 11.6505
137 4LZJ 22H 0.0275 0.41212 12.2112
138 2Q8Z NUP 0.01228 0.41945 12.8655
139 4B5W PYR 0.0002821 0.53206 12.8906
140 3CF6 SP1 0.01379 0.42244 13.7725
141 3E85 BSU 0.006599 0.45146 13.9241
142 1M5W DXP 0.04171 0.40973 17.6955
143 5UKL SIX 0.02582 0.40727 19.3548
144 2BGS NDP 0.03758 0.40316 19.4767
145 1V3S ATP 0.01435 0.42148 19.8276
Pocket No.: 11; Query (leader) PDB : 2G50; Ligand: ALA; Similar sites found: 25
This union binding pocket(no: 11) in the query (biounit: 2g50.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4ADC PLP 0.03434 0.40185 1.72414
2 5THY SAH 0.02216 0.40891 1.7284
3 2XGT NSS 0.02501 0.41274 1.83908
4 4KRI SAH 0.02007 0.41196 2.30947
5 1H74 ADP 0.04321 0.40633 2.36486
6 1EU1 MGD 0.04959 0.40807 2.64151
7 3LU1 NAD 0.04347 0.40208 2.74725
8 2FXV 5GP 0.01951 0.41506 3.09278
9 4D86 ADP 0.01535 0.41528 3.37349
10 3GBR PRP 0.03964 0.40729 3.47826
11 1NV8 SAM 0.03838 0.4029 3.52113
12 4OOP DUP 0.0332 0.40087 4.21687
13 3MB5 SAM 0.02288 0.41059 4.70588
14 3F4F UMP 0.01823 0.40622 5.38922
15 5CIC 51R 0.004567 0.41204 5.55556
16 1NAA 6FA 0.04902 0.41127 5.66038
17 1SB8 UD2 0.04516 0.42029 6.81818
18 1SB8 NAD 0.04037 0.42029 6.81818
19 5A5W GUO 0.04619 0.41036 7.50988
20 2PHN GDP 0.02369 0.40938 9.44882
21 4LXQ FON 0.03056 0.41648 9.48905
22 4LXQ TYD 0.03056 0.41648 9.48905
23 1EJB INJ 0.01982 0.40645 9.52381
24 5CUQ NSC 0.02346 0.42022 11.6105
25 5UKL SIX 0.03522 0.40351 19.3548
Pocket No.: 12; Query (leader) PDB : 2G50; Ligand: ALA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 2g50.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 2G50; Ligand: ALA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 2g50.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 2G50; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 2g50.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 15; Query (leader) PDB : 2G50; Ligand: ALA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 15) in the query (biounit: 2g50.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 16; Query (leader) PDB : 2G50; Ligand: PYR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 16) in the query (biounit: 2g50.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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